General stats output - Githubissues

ohnosequences / mg7

Configurable and scalable 16S metagenomics data analysis

https://goo.gl/y3rZFD

GNU Affero General Public License v3.0

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General stats output #9

Closed laughedelic closed 8 years ago

laughedelic commented 8 years ago

We need a CSV file of the stats with the following format:

sample ID
[ ] total number of input pair-end reads (total number of input pairs)
[x] number of merged reads
[ ] number of not merged reads
[x] number of no-blast-hits
[ ] number of assigned reads
[x] number of not assigned reads

marina-manrique commented 8 years ago

@laughedelic we also need the number of reads with No Hits

marina-manrique commented 8 years ago

No Blast Hits

laughedelic commented 8 years ago

@marina-manrique I've added an output file with all reads (headers) that didn't get BLAST hits. Do you need only the number or their headers are useful too?

laughedelic commented 8 years ago

Things that are counted explicitly:

total input (paired-end) reads
number of flash-merged reads
number of flash-not-merged reads
number of no-blast-hits reads (+ file with them)
number of not assigned reads (+ file with them/their IDs)

And I'm adding flash-not-merged reads output files.

marina-manrique commented 8 years ago

Do you need only the number or their headers are useful too?

headers are useful as well

laughedelic commented 8 years ago

This seems to be finished. Nothing's tested yet, but let's be optimistic! :tada: